Structure analysis of

After successful structure solution and refinement, the final and very important phase completes the structural analysis. This is the detailed inspection of the structure looking for the intramolecular and intermolecular structural features of the system studied. Traditionally a plot of the molecule or a representative part of the structure (in a case continuous structures, like metallo-organic or organic frameworks, MOF or OF, respectively) with thermal ellipsoids viz. anisotropic displacement parameters) is presented. Such a plot drawn using program ORTEP [23] for compound 1 is presented in Fig. 9.12 (top). 

To show the total size of the molecule and to illustrate intramolecular interactions such as hydrogen bonds, a plot is best used where atoms are drawn with their van der Waals radii (CPK model. Fig. 9.12, bottom). 

Compound 1 shows many intermolecular interactions. Firstly, the packing plot (but also the 3-D atom coordinate list) reveals that no solvent molecules are included in the crystal lattice. The crystallization was done from ethanol, but ethanol molecules are not included into the crystal lattice. The packing plot (Fig. 9.14) shows that an intermolecular interaction between the moledues, i.e. re-re stacking, creates an antiparallel pair of 1 with short non-bonded contact distance of 3.30 A 

The easiest way to inspect the structure (in addition to the tables mentioned above) utilizes graphical representations of the structure on a computer screen. Some very nice and easy to use crystallographic graphics programs are available in the Internet. One such a program is Mercury, provided by Cambridge Crystallographic Data Centre (http //www.ccdc.cam.ac.uk/products/csd system/mercury/ downloads/). 

The solid state X-ray structure will also give information about the configurational, stereochemical or tautomeric information about the studied structure. In the case of optically pure compounds, the absolute configuration of an unknown compound can be obtained, if the molecule studied contains at least one heavier element (like Cl, S, or metal ion) per 20 carbon atoms. If compound 1 would be optically active, the chlorine atom would enable the determination of the absolute configuration. 

---

However, recent advances in teclmiques will ensure fiirther diversification and complexification of solved surface structures. The present maturity of teclmiques will thus iucreasmgly allow the analysis of structures chosen for their practical interest rather than for their simplicity. 

Fetisova Z G, Borisov A Y and Fok M V 1985 Analysis of structure-function correlations in light-harvesting photosynthetic antenna—structure optimization parameters J. Theoret. Biol. 112 41-75... 

Visuahzation and analysis of structure and dynamics simulation results. Free of charge for academic use. Available for different platforms. Imports TINKER results and accepts various file formats. hitp //www.csc.ji/gopenmol/... 

Kubinyi H 1995. The Quantitative Analysis of Structure-Activity Relationships. In Wolff M E (Editor) Burger s Medicinal Chemistry and Drug Discovery. 5th Edition, Volume 1. New York, John Wiley Sons, pp. 497-571. 

Freudentlial, A. M., Garrelts, J. M. and Sliinozuka, M. 1966 The Analysis of Structural Safety. Journal of the Structural Division, American Society of Civil Engineers, 92, STl, 261-MS. 

Baum, M. R. 1987. Disruptive failure of pressure vessels preliminary design guide lines for fragment velocity and the extent of the hazard zone. In Advances in Impact, Blast Ballistics, arui Dynamic Analysis of Structures. ASME PVP. 124. New York ASME. 

Fujita, T., and Iwamura, H. Applications of Various Steric Constants to Quantitative Analysis of Structure-Activity Relationshipf, 114, 119-157 (1983). 

Combined analysis of structural and genomic data will certainly get more importance in the near future. Protein folds can be analysed for whole genomes. 

The correlation of structural and vibrational parameters, and a detailed analysis of structural trends based on the available wealth of electron diffraction, microwave and X-ray structural studies on sulphoxides and sulphones, have been reported by Hargittai in a comprehensive study20 which will stand for a long time as a milestone in the structural... 

Margalit H. Fisher N. Ben-Sasson S.A. (1993) Comparative analysis of structurally defined heparin binding sequences reveals a distinct spatial distribution of basic residues // J. Biol. Chem V. 268. P.19228-19231. 

Szklarz GD, Halpert JR. Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450. Life Sci 1997 61 2507-20. 

Chui, Y.H., Snook, I.K. and Russo, S.P. (2007) Visualization and analysis of structural ordering during crystallization of a gold nanoparticle. Physical Review B -Condensed Matter, 76,195427-1—195427-6. 

G. Calomme and P.J. Lewi, Multivariate analysis of structure-activity data. Spectral map of opioid narcotics in receptor binding. Actual. Chim. Therap., S.l 1 (1984) 121-126. 

Somsen et al. [796] have reported the use of SERR spectroscopy for the in situ selective determination and semi-quantitative analysis of structurally similar dyes separated by TLC. The limits of identification of the TLC-SERRS method (ca. 5ng applied) were sufficient for acquisition of spectra of impurities present in the certified dye standards. SERRS may also be used for in situ identification of highly fluorescent molecules on HPTLC plates. 

Characterisation covers a wide field of science and technology and interacts from the synthesis stage through the analysis of structure to the determination of properties. Characterisation allows one to observe, control and model (including "closed-loop" backward interaction) all the complex interrelationships of materials science. 

SRSAXS is utilized, because the scattering curve measured in symmetrical reflection is readily transformed into a ID scattering curve, I (53). The importance of such curves for the analysis of structure has been demonstrated in the preceding sections of this chapter. 

Blanc, V. Lagneaux, D. Dider, P., et al., Cloning and analysis of structural genes from streptomyces pristinaspirales encoding enzymes involved in the conversion of pristinamycin PUB to PIIA PIIA synthase and NADH riboflavin 5 phosphate oxidoreductase. 1995, 177, 5206-5214. 

T.J. Wess, M. Drakopoulos, A. Snigirev, J. Wounters, O. Paris, P. Fratzl, M. Collins, J. Hiller, K. Nielsen, The Use of Small Angle X Ray Diffraction Studies for the Analysis of Structural Features in Archaeological Samples, Archaeometry, 43, 117 129 (2001). 

A complication in the analysis of structural data is the growing recognition that the involvement of metal cations with a ligand s 7t-electrons (often in aromatic rings) can give rise to various structural distortions. Such cation-7t... 

The quantitative analysis of structure-reactivity relationships and the measurements of significant p-values for ring substituent effects on arylolefins must take into account several related problems ... 

---